| 1. |
- López, J L, et al.
(författare)
-
Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions.
- 2017
-
Ingår i: FEMS Microbiology Ecology. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 93:1
-
Tidskriftsartikel (refereegranskat)abstract
- Rhodopsins are broadly distributed. In this work we analyzed 23 metagenomes corresponding to marine sediment samples from four regions which share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral-rodopsins, an initial set of 6224 bacterial rhodopsins sequences according COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment 123 viral (51) and non-viral (72) sequences (>50 aminoacids) were finally included in further analysis. Viral rhodopsin genes were homologues of Phaeocystis globosa virus and Organic lake Phycodnavirus Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus as well as Cryptophyta and Fungi. A re-screening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 aminoacids). Phylogeographic analysis revealed a geographycal clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsins (PAVR) genes related to Actinobacteria and Chloroflexi This is the first report about the existence of a phylogeographic association of the viral rhodopsins sequences from marine sediments.
|
|
| 2. |
- Thompson, Luke R., et al.
(författare)
-
A communal catalogue reveals Earth's multiscale microbial diversity
- 2017
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 551:7681, s. 457-463
-
Tidskriftsartikel (refereegranskat)abstract
- © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
|
|
| 3. |
|
|
| 4. |
- Elväng, Annelie M., et al.
(författare)
-
Use of green fluorescent protein and luciferase biomarkers to monitor survival and activity of Arthrobacter chlorophenolicus A6 cells during degradation of 4-chlorophenol in soil
- 2001
-
Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 3:1, s. 32-42
-
Tidskriftsartikel (refereegranskat)abstract
- The recently isolated novel species Arthrobacter chlorophenolicus A6 is capable of growth on and degradation of high concentrations of 4-chlorophenol (up to 350 mug ml(-1)) as the sole carbon and energy source, This strain shows promise for bioremediation of environmental sites contaminated with high levels of chlorophenols. In this study, green fluorescent protein (gfp) or luciferase (luc) genes were used as biomarkers for monitoring cell number and activity, respectively, during degradation of 4-chlorophenol by A. chlorophenolicus cells. The individual marked strains, Arthrobacter chlorophenolicus A6L (luc-tagged) and Arthrobacter chlorophenolicus A6G (gfp-tagged), were monitored during degradation of 250 mug ml(-1) 4-chlorophenol in pure culture and 175 mug g(-1) 4-chlorophenol in soil microcosms. Both gene-tagged strains were capable of cleaning up the contaminated soil during 9 d incubation. During the bioremediation experiments, the luc-tagged cells were monitored using luminometry and the gfp tagged cells using flow cytometry, in addition to selective plate counting for both strains. The cells remained at high population levels in the soil (evidenced by GFP-fluorescent cell counts) and the A. chlorophenolicus A6L population was metabolically active (evidenced by luciferase activity measurements). These results demonstrate that the Arthrobacter chlorophenolicus A6 inoculum is effective for cleaning-up soil containing high concentrations of 4-chlorophenol.
|
|
| 5. |
- Espínola, Fernando, et al.
(författare)
-
Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes
- 2018
-
Ingår i: Microbial Ecology. - : Springer. - 0095-3628 .- 1432-184X. ; :1, s. 123-139
-
Tidskriftsartikel (refereegranskat)abstract
- In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.
|
|
| 6. |
- Hammarström, Per, 1960-
(författare)
-
Nationens styvbarn : Judisk samhällsintegration i några Norrlandsstäder 1870-1940
- 2007
-
Ingår i: Svensk kyrkotidning. - Stockholm : Carlsson Bokförlag. - 0346-2153. ; :51-52, s. 664-
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Syftet med denna avhandling är att undersöka vilken ekonomisk och social ställning den judiska minoriteten intog i det svenska samhället under perioden 1870 till 1940. Tidigare forskning har riktat stor uppmärksamhet mot rättsliga och politiska aspekter av den svenska judenhetens historia, mer sällan mot judarna och samhället i en bredare bemärkelse. Andra studier har lyft fram antisemitism på svensk mark utan att koppla fenomenet till en social nivå.Genom en undersökning av hur judiska invandrare, med ursprung i Östeuropa, successivt fogades in i några svenska lokalsamhällen, tar denna avhandling ett bredare grepp på frågan om judarna och samhället. Här undersöks hur den svenska judenheten integrerades i samhället efter det att emancipationen gett judarna fulla medborgerliga och politiska rättigheter. Judarnas ekonomiska och sociala ställning undersöks, liksom den sociala antisemitism som drabbade judarna. Studien rör sig i gränslandet mellan social- och kulturhistoria. Undersökningen visar att merparten av judarna i Sundsvall, en betydelsefull handelsstad i norra Sverige, fick sin försörjning genom en föga lönsam gårdfarihandel under början av undersökningsperioden. Sedan butiks- och grosshandelsrörelser började grundas inleddes en långsam socioekonomisk klättring. I takt med de ekonomiska framgångarna ökade judarnas sociala status, med engagemang i föreningslivet och lokalpolitiken. De framgångsrika familjerna tonade ner sin judiska identitet till förmån för en borgerlig och nationell kultur.Ungefär hälften av den judiska gruppen fick aldrig uppleva framgången utan förblev en marginaliserad grupp, med småhantverk eller gårdfarihandel som försörjningsbas. Det stora flertalet av denna underklass saknade svenskt medborgarskap. En social klyfta vidgades gentemot den judiska borgerligheten. Under hela undersökningsperioden var antisemitismen en kulturell kod i majoritetssamhället, oavsett integration och socioekonomisk framgång. Mycket tyder på att det sociala klimatet blev mer fientligt gentemot judarna efter 1920. Studien visar att nationalstaten Sverige lämnade litet utrymme för multikulturella strukturer. Judarna accepterades som nationens styvbarn men knappast som fullvärdiga svenskar.
|
|
| 7. |
- Jansson, Peter M., Filosofie Doktor, 1965-, et al.
(författare)
-
The Interaction of Ideology and Institutions in Treating Violent Men in Sweden
- 2022
-
Ingår i: Social Work & Social Sciences Review. - London : Whiting & Birch, Ltd.. - 0953-5225 .- 1746-6105. ; 22:3, s. 23-35
-
Tidskriftsartikel (refereegranskat)abstract
- Since Sweden has a reputation for having a pragmatic, technocratic approach to solving social problems, the question arises as to why the country uses different methods at the national and the local level for treating violent men. If studies show that one method is superior to others, we would expect both levels of government to use similar treatment methods. Despite the emphasis on pragmatic solutions, ideology plays an important role, as the Swedish government in recent decades has largely accepted the New Public Management approach to governance. However, because of differences in institutional arrangements, it becomes logically appropriate for the national level to utilize a different type of therapy (Cognitive Behavioral Therapy) than the local level (Psycho Dynamic Therapy among others). Thus, a combination of an ideological shift to New Public Management and institutional differences can explain the differences in therapeutic approaches, rather than reliance on scientific studies.
|
|
| 8. |
- Lowder, M, et al.
(författare)
-
Effect of starvation and the viable-but-nonculturable state on green fluorescent protein (GFP) fluorescence in GFP-tagged Pseudomonas fluorescens A506
- 2000
-
Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 66:8, s. 3160-3165
-
Tidskriftsartikel (refereegranskat)abstract
- The green fluorescent protein (GFP) gene, gfp, of the jellyfish Aequorea victoria is being used as a reporter system for gene expression and as a marker for tracking prokaryotes and eukaryotes. Cells that have been genetically altered with the gfp gene produce a protein that fluoresces when it is excited by UV light. This unique phenotype allows gth-tagged cells to be specifically monitored by nondestructive means, In this study we determined whether a gfp-tagged strain of Pseudomonas fluorescens continued to fluoresce under conditions under which the cells were starved, viable but nonculturable (VBNC), or dead. Epifluorescent microscopy, flow cytometry, and spectrofluorometry were used to measure fluorescence intensity in starved, VBNC, and dead or dying cells. Results obtained by using how cytometry indicated that microcosms containing VBNC cells, which were obtained by incubation under stress conditions (starvation at 37.5 degrees C), fluoresced at an intensity that mas at least 80% of the intensity of nonstressed cultures, Similarly, microcosms containing starved cells incubated at 5 and 30 degrees C had fluorescence intensities that were 90 to 110% of the intensity of nonstressed cells. VBNC cells remained fluorescent during the entire 6-month incubation period. in addition, cells starved at 5 or 30 degrees C remained fluorescent for at least 11 months. Treatment of the cells with UV light or incubation at 39 or 50 degrees C resulted in a loss of GFP from the cells. There was a strong correlation between cell death and leakage of GFP from the cells, although the extent of leakage varied depending on the treatment, Most dead cells were not GFP fluorescent, but a small proportion of the dead cells retained some GFP at a lower concentration than the concentration in live cells, Our results suggest that gfp-tagged cells remain fluorescent following starvation and entry into the VBNC state but that fluorescence is lost when the cells die, presumably because membrane integrity is lost.
|
|
| 9. |
- Lu, Zexun, et al.
(författare)
-
In vivo study of Trichoderma-pathogen-plant interactions, using constitutive and inducible green fluorescent protein reporter systems
- 2004
-
Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 70:5, s. 3073-3081
-
Tidskriftsartikel (refereegranskat)abstract
- Plant tissue colonization by Trichoderma atroviride plays a critical role in the reduction of diseases caused by phytopathogenic fungi, but this process has not been thoroughly studied in situ. We monitored in Situ interactions between gfp-tagged biocontrol strains of T. atroviride and soilborne plant pathogens that were grown in cocultures and on cucumber seeds by confocal scanning laser microscopy and fluorescence stereomicroscopy. Spores of T. atroviride adhered to Pythium ultimum mycelia in coculture experiments. In mycoparasitic interactions of T. atroviride with P. ultimum or Rhizoctonia solani, the mycoparasitic hyphae grew alongside the pathogen mycelia, and this was followed by coiling and formation of specialized structures similar to hooks, appressoria, and papillae. The morphological changes observed depended on the pathogen tested. Branching of T. atroviride mycelium appeared to be an active response to the presence of the pathogenic host. Mycoparasitism of P. ultimum by T. atroviride occurred on cucumber seed surfaces while the seeds were germinating. The interaction of these fungi on the cucumber seeds was similar to the interaction observed in coculture experiments. Green fluorescent protein expression under the control of host-inducible promoters was also studied. The induction of specific Trichoderma genes was monitored visually in cocultures, on plant surfaces, and in soil in the presence of colloidal chitin or Rhizoctonia by confocal microscopy and fluorescence stereomicroscopy. These tools allowed initiation of the mycoparasitic gene expression cascade to be monitored in vivo.
|
|
| 10. |
- Matos, Marina N., et al.
(författare)
-
Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments
- 2016
-
Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 18:12, s. 4471-4484
-
Tidskriftsartikel (refereegranskat)abstract
- Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.
|
|
